Before I start getting in depth with this post, let me first say please, please, put down the package of Gerber prefolds that you picked up at Target, Babies R Us, or Wal-mart. While these are labeled as "diapers" and they look like any other prefold, they are really only good as spit up cloths and dust rags. The reason is because of what's in them. For some "only-God-knows-why" reason, Gerber makes their prefolds stuffed with polyfill rather than absorbent cotton. Pollyfill is a non-absorbent (worse than non-absorbent, it is water repelling!) polyester "stuffing" type material. Think about what you used in your junior high home-ec class to stuff that pillow; that was most likely polyfill. Good for teddybears, car upholstry, and cheap home-ec projects, crappy for diapers.
You want to make sure you buy prefolds that are 100% absorbent material. Cotton will be the most common and budget-friendly material that you find, but you could also find hemp or bamboo prefolds as well. I have used all three and honestly have not noticed a difference in absorbency or performence. The bamboo is a little softer, and the hemp feels a little heavier/more dense, but all three work about the same. You also want to make sure that you are buying Diaper Service Quality (DSQ) prefolds. This is just to make sure they meet a high quality standard, even if you are not planning on using a diaper service to launder them.
If you decide to go with cotton, you need to choose white or unbleached. The white (bleached) have had natural oils stripped away from them using chemicals, and are a bright white. Unbleached are a natural brownish-color. You do have to wash unbleached diapers a bit more while "prepping" them for use, to wash out their natural oils. I have personally noticed that my unbleached cotton prefolds are softer than my bleached cotton prefolds. If I buy bleached, I try to make sure that the fabric was processed with a peroxide bath, not chlorine. This is for ecological as well as skin-health reasons. Chlorine bleaching makes a mess in our environment, and I'd rather not have the remnants of the process sitting next to my baby's delicate parts.
My two top picks for prefold diapers are Green Mountain Diapers, who sell Cloth-eez prefolds, and Cottonbabies Econobums. Neither of these companies have given me compensation, nor am I affiliated with them in any way aside from using their products on a daily (hourly?) basis.
Green Mountain Diapers have been my go-to since Jonah was a little bean growing inside of me. They offer several sized prefolds, all of them color coded so that if you need more, you don't have to remember what size you bought, just the color. My babies have both spent the majority of their lives (okay, so Evie that would be her whole life) in the red edged, or 15.5"x18.5" Even though these are their "medium" size, they are easily folded to fit newborns, and I just expand the folds as they grow. Admittedly, I do not have huge babies, Evie weighing in at just 15 lbs at 8 months. Jonah was 23 lbs and about 18 months when we sized up to the brown edged.
I also like that Green Mountain Diapers uses a peroxide bath to bleach their diapers, rather than chlorine. I like their price and quality, as well as their customer service.
Cottonbabies Econobum is relatively new. I do not own any, because they were not around when I was buying my prefolds. However I do have experience with them through children I've babysat and my friends' children. The first time that I picked one up and held it in my hand, my first thoughts were that they do not seem as "heavy duty" as the Green Mountain Diapers. They are much lighter, and I'm wondering what their condition will be years and years down the line. Two things I like about these diapers: their price, and the company. The full kit includes 12 prefolds, three one size covers, and a wetbag for $48.95. They can be found at Babies R Us,which means you can use one of their wonderful coupons that they always mail out, to make them even cheaper. The company, Cottonbabies, is always trying to improve their design and product. I've had wonderful customer service from them, and they really seem to listen to what their consumer base needs and wants. If I had to buy an entire diaper "stash" all over again, I would definitely get one of these boxes!
One thing you will want to make sure to pick up with any prefold order, no matter where you purchase from, is a snappi. A snappi is a great way to secure a diaper without needing to learn how to pin while holding down a squirmy baby. I've tried pins before, and while my diapers looked beautiful on my practice baby dolls, I could never get the same result on my twisty turny rolling spinning babies. I love my snappis! Here is a quick video demonstrating how to fasten one. Please excuse my fumbling around; I gave the camera man a day off!